Multiple sequence alignment - TraesCS5A01G508900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G508900 chr5A 100.000 2964 0 0 1 2964 673237894 673240857 0.000000e+00 5474.0
1 TraesCS5A01G508900 chr5A 74.534 161 39 2 2791 2950 32672947 32673106 5.300000e-08 69.4
2 TraesCS5A01G508900 chr2A 98.049 2255 32 5 1 2249 776173547 776175795 0.000000e+00 3910.0
3 TraesCS5A01G508900 chr2A 97.719 2280 36 5 1 2274 9951377 9953646 0.000000e+00 3908.0
4 TraesCS5A01G508900 chr1A 96.447 2280 63 9 1 2271 532735320 532733050 0.000000e+00 3746.0
5 TraesCS5A01G508900 chr1A 93.354 1956 97 11 1 1952 584970314 584972240 0.000000e+00 2861.0
6 TraesCS5A01G508900 chr1A 96.429 1260 38 3 3 1262 12307863 12309115 0.000000e+00 2071.0
7 TraesCS5A01G508900 chr1A 93.693 983 37 5 1299 2274 12309363 12310327 0.000000e+00 1448.0
8 TraesCS5A01G508900 chr1A 91.265 332 21 4 1946 2271 584972292 584972621 2.100000e-121 446.0
9 TraesCS5A01G508900 chr3A 94.961 2282 67 14 1 2268 698295942 698298189 0.000000e+00 3533.0
10 TraesCS5A01G508900 chr7B 93.804 1953 87 11 1 1952 706976362 706974443 0.000000e+00 2905.0
11 TraesCS5A01G508900 chr3B 92.945 1956 97 12 1 1952 772227379 772229297 0.000000e+00 2809.0
12 TraesCS5A01G508900 chr5B 92.913 1933 102 14 25 1952 26737059 26735157 0.000000e+00 2778.0
13 TraesCS5A01G508900 chr5B 91.867 332 19 5 1946 2271 26735105 26734776 9.680000e-125 457.0
14 TraesCS5A01G508900 chr5B 80.380 158 18 2 2715 2861 691284053 691283898 1.120000e-19 108.0
15 TraesCS5A01G508900 chr1B 91.607 1954 107 13 1 1952 182058520 182060418 0.000000e+00 2647.0
16 TraesCS5A01G508900 chr1B 90.691 333 24 3 1946 2271 182060466 182060798 1.260000e-118 436.0
17 TraesCS5A01G508900 chrUn 94.597 944 41 6 1010 1952 117079696 117080630 0.000000e+00 1452.0
18 TraesCS5A01G508900 chrUn 92.341 927 59 6 1 925 117078752 117079668 0.000000e+00 1308.0
19 TraesCS5A01G508900 chrUn 89.666 329 28 4 1950 2272 290195665 290195993 5.910000e-112 414.0
20 TraesCS5A01G508900 chr4D 83.260 454 49 6 2536 2964 493924653 493925104 2.770000e-105 392.0
21 TraesCS5A01G508900 chr4D 81.466 232 30 3 2644 2864 421983951 421983722 8.440000e-41 178.0
22 TraesCS5A01G508900 chr4D 82.659 173 29 1 2787 2959 175192672 175192843 5.120000e-33 152.0
23 TraesCS5A01G508900 chr4D 97.619 42 1 0 2272 2313 493924132 493924173 4.100000e-09 73.1
24 TraesCS5A01G508900 chr4A 82.941 340 45 8 2634 2964 201595714 201596049 8.030000e-76 294.0
25 TraesCS5A01G508900 chr4A 88.732 71 6 1 2722 2792 618241098 618241030 5.260000e-13 86.1
26 TraesCS5A01G508900 chr2D 82.991 341 42 10 2634 2963 71426408 71426073 8.030000e-76 294.0
27 TraesCS5A01G508900 chr2D 86.364 110 13 2 2823 2932 444557399 444557506 5.190000e-23 119.0
28 TraesCS5A01G508900 chr2B 79.240 342 53 9 2634 2964 662679758 662679424 3.850000e-54 222.0
29 TraesCS5A01G508900 chr2B 81.413 269 32 8 2643 2897 252101999 252101735 1.390000e-48 204.0
30 TraesCS5A01G508900 chr5D 77.745 337 58 7 2639 2962 547537914 547537582 1.080000e-44 191.0
31 TraesCS5A01G508900 chr7D 77.744 328 51 9 2641 2951 305099065 305098743 6.530000e-42 182.0
32 TraesCS5A01G508900 chr1D 76.526 213 35 6 2732 2931 426648090 426648300 5.230000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G508900 chr5A 673237894 673240857 2963 False 5474.00 5474 100.0000 1 2964 1 chr5A.!!$F2 2963
1 TraesCS5A01G508900 chr2A 776173547 776175795 2248 False 3910.00 3910 98.0490 1 2249 1 chr2A.!!$F2 2248
2 TraesCS5A01G508900 chr2A 9951377 9953646 2269 False 3908.00 3908 97.7190 1 2274 1 chr2A.!!$F1 2273
3 TraesCS5A01G508900 chr1A 532733050 532735320 2270 True 3746.00 3746 96.4470 1 2271 1 chr1A.!!$R1 2270
4 TraesCS5A01G508900 chr1A 12307863 12310327 2464 False 1759.50 2071 95.0610 3 2274 2 chr1A.!!$F1 2271
5 TraesCS5A01G508900 chr1A 584970314 584972621 2307 False 1653.50 2861 92.3095 1 2271 2 chr1A.!!$F2 2270
6 TraesCS5A01G508900 chr3A 698295942 698298189 2247 False 3533.00 3533 94.9610 1 2268 1 chr3A.!!$F1 2267
7 TraesCS5A01G508900 chr7B 706974443 706976362 1919 True 2905.00 2905 93.8040 1 1952 1 chr7B.!!$R1 1951
8 TraesCS5A01G508900 chr3B 772227379 772229297 1918 False 2809.00 2809 92.9450 1 1952 1 chr3B.!!$F1 1951
9 TraesCS5A01G508900 chr5B 26734776 26737059 2283 True 1617.50 2778 92.3900 25 2271 2 chr5B.!!$R2 2246
10 TraesCS5A01G508900 chr1B 182058520 182060798 2278 False 1541.50 2647 91.1490 1 2271 2 chr1B.!!$F1 2270
11 TraesCS5A01G508900 chrUn 117078752 117080630 1878 False 1380.00 1452 93.4690 1 1952 2 chrUn.!!$F2 1951
12 TraesCS5A01G508900 chr4D 493924132 493925104 972 False 232.55 392 90.4395 2272 2964 2 chr4D.!!$F2 692

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
718 739 0.536006 GATGTATGCAGAGCCCCACC 60.536 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2798 0.107508 CACACCATCCGAGCCAGAAT 60.108 55.0 0.0 0.0 0.0 2.4 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
493 514 3.912907 GAGGGCGCGGCTAGCTAA 61.913 66.667 32.30 0.00 45.59 3.09
718 739 0.536006 GATGTATGCAGAGCCCCACC 60.536 60.000 0.00 0.00 0.00 4.61
719 740 1.281199 ATGTATGCAGAGCCCCACCA 61.281 55.000 0.00 0.00 0.00 4.17
720 741 1.452108 GTATGCAGAGCCCCACCAC 60.452 63.158 0.00 0.00 0.00 4.16
1059 1089 2.734492 CGTCCTCGAAAACTTCCGCTAT 60.734 50.000 0.00 0.00 39.71 2.97
1341 1582 6.814506 ATTTCAGAGGACACTTGAAATCTG 57.185 37.500 6.00 0.00 35.15 2.90
1997 2334 3.452264 ACCATAGACTGCTAGATGTTGCA 59.548 43.478 0.00 0.00 37.63 4.08
2103 2442 5.843969 TCTGTTACATCCCAGCTATTATGGA 59.156 40.000 0.00 0.00 40.51 3.41
2159 2498 1.847890 GCCGTAGCAAAAACGAGCCA 61.848 55.000 0.00 0.00 42.90 4.75
2335 2704 3.683518 GGGCTGGGGATTTGGGGT 61.684 66.667 0.00 0.00 0.00 4.95
2338 2707 2.364160 CTGGGGATTTGGGGTGGG 59.636 66.667 0.00 0.00 0.00 4.61
2339 2708 2.455532 TGGGGATTTGGGGTGGGT 60.456 61.111 0.00 0.00 0.00 4.51
2340 2709 2.038813 GGGGATTTGGGGTGGGTG 59.961 66.667 0.00 0.00 0.00 4.61
2341 2710 2.858655 GGGATTTGGGGTGGGTGT 59.141 61.111 0.00 0.00 0.00 4.16
2342 2711 1.609210 GGGATTTGGGGTGGGTGTG 60.609 63.158 0.00 0.00 0.00 3.82
2343 2712 1.155155 GGATTTGGGGTGGGTGTGT 59.845 57.895 0.00 0.00 0.00 3.72
2344 2713 1.184970 GGATTTGGGGTGGGTGTGTG 61.185 60.000 0.00 0.00 0.00 3.82
2345 2714 1.152355 ATTTGGGGTGGGTGTGTGG 60.152 57.895 0.00 0.00 0.00 4.17
2350 2719 3.503839 GGTGGGTGTGTGGGGGAA 61.504 66.667 0.00 0.00 0.00 3.97
2351 2720 2.115266 GTGGGTGTGTGGGGGAAG 59.885 66.667 0.00 0.00 0.00 3.46
2352 2721 3.182263 TGGGTGTGTGGGGGAAGG 61.182 66.667 0.00 0.00 0.00 3.46
2353 2722 4.678743 GGGTGTGTGGGGGAAGGC 62.679 72.222 0.00 0.00 0.00 4.35
2355 2724 2.034221 GTGTGTGGGGGAAGGCTC 59.966 66.667 0.00 0.00 0.00 4.70
2356 2725 3.256960 TGTGTGGGGGAAGGCTCC 61.257 66.667 0.00 0.00 41.59 4.70
2357 2726 3.256960 GTGTGGGGGAAGGCTCCA 61.257 66.667 0.00 0.00 44.51 3.86
2358 2727 2.451493 TGTGGGGGAAGGCTCCAA 60.451 61.111 0.00 0.00 44.51 3.53
2360 2729 1.076705 GTGGGGGAAGGCTCCAATC 60.077 63.158 0.00 0.00 44.51 2.67
2361 2730 2.193248 GGGGGAAGGCTCCAATCG 59.807 66.667 0.00 0.00 44.51 3.34
2362 2731 2.375345 GGGGGAAGGCTCCAATCGA 61.375 63.158 0.00 0.00 44.51 3.59
2363 2732 1.607612 GGGGAAGGCTCCAATCGAA 59.392 57.895 0.00 0.00 44.51 3.71
2365 2734 1.420138 GGGGAAGGCTCCAATCGAATA 59.580 52.381 0.00 0.00 44.51 1.75
2366 2735 2.495084 GGGAAGGCTCCAATCGAATAC 58.505 52.381 0.00 0.00 44.51 1.89
2368 2737 3.134458 GGAAGGCTCCAATCGAATACTG 58.866 50.000 0.00 0.00 41.96 2.74
2369 2738 3.432326 GGAAGGCTCCAATCGAATACTGT 60.432 47.826 0.00 0.00 41.96 3.55
2370 2739 4.202223 GGAAGGCTCCAATCGAATACTGTA 60.202 45.833 0.00 0.00 41.96 2.74
2371 2740 4.592485 AGGCTCCAATCGAATACTGTAG 57.408 45.455 0.00 0.00 0.00 2.74
2372 2741 3.060602 GGCTCCAATCGAATACTGTAGC 58.939 50.000 0.00 0.00 0.00 3.58
2374 2743 2.726760 CTCCAATCGAATACTGTAGCGC 59.273 50.000 0.00 0.00 0.00 5.92
2375 2744 2.100087 TCCAATCGAATACTGTAGCGCA 59.900 45.455 11.47 0.00 0.00 6.09
2376 2745 2.218759 CCAATCGAATACTGTAGCGCAC 59.781 50.000 11.47 6.60 0.00 5.34
2377 2746 2.857748 CAATCGAATACTGTAGCGCACA 59.142 45.455 11.47 11.35 35.30 4.57
2378 2747 2.640346 TCGAATACTGTAGCGCACAA 57.360 45.000 11.47 0.00 36.48 3.33
2379 2748 2.256174 TCGAATACTGTAGCGCACAAC 58.744 47.619 11.47 5.27 36.48 3.32
2381 2750 2.222508 CGAATACTGTAGCGCACAACAC 60.223 50.000 11.47 0.00 36.48 3.32
2382 2751 2.743636 ATACTGTAGCGCACAACACT 57.256 45.000 11.47 2.73 36.48 3.55
2384 2753 0.179084 ACTGTAGCGCACAACACTGT 60.179 50.000 11.47 6.50 36.48 3.55
2386 2755 1.455786 CTGTAGCGCACAACACTGTAC 59.544 52.381 11.47 0.00 36.48 2.90
2387 2756 0.433492 GTAGCGCACAACACTGTACG 59.567 55.000 11.47 0.00 43.82 3.67
2388 2757 0.665068 TAGCGCACAACACTGTACGG 60.665 55.000 11.47 0.00 41.72 4.02
2390 2759 1.300311 CGCACAACACTGTACGGGA 60.300 57.895 6.65 0.00 38.44 5.14
2391 2760 1.554042 CGCACAACACTGTACGGGAC 61.554 60.000 6.65 0.00 38.44 4.46
2392 2761 0.249741 GCACAACACTGTACGGGACT 60.250 55.000 6.65 0.00 33.22 3.85
2393 2762 1.497991 CACAACACTGTACGGGACTG 58.502 55.000 6.65 2.38 33.22 3.51
2394 2763 1.117150 ACAACACTGTACGGGACTGT 58.883 50.000 6.65 0.00 40.59 3.55
2395 2764 2.034939 CACAACACTGTACGGGACTGTA 59.965 50.000 6.65 0.00 38.09 2.74
2396 2765 2.295349 ACAACACTGTACGGGACTGTAG 59.705 50.000 6.65 1.32 38.09 2.74
2397 2766 2.555325 CAACACTGTACGGGACTGTAGA 59.445 50.000 6.65 0.00 38.09 2.59
2398 2767 2.157738 ACACTGTACGGGACTGTAGAC 58.842 52.381 6.65 0.00 38.09 2.59
2399 2768 1.471684 CACTGTACGGGACTGTAGACC 59.528 57.143 6.65 0.00 38.09 3.85
2405 2774 3.808583 GGGACTGTAGACCGAACAC 57.191 57.895 0.00 0.00 0.00 3.32
2406 2775 1.254954 GGGACTGTAGACCGAACACT 58.745 55.000 0.00 0.00 0.00 3.55
2407 2776 1.067776 GGGACTGTAGACCGAACACTG 60.068 57.143 0.00 0.00 0.00 3.66
2408 2777 1.612463 GGACTGTAGACCGAACACTGT 59.388 52.381 0.00 0.00 0.00 3.55
2409 2778 2.035576 GGACTGTAGACCGAACACTGTT 59.964 50.000 0.00 0.00 0.00 3.16
2410 2779 3.306818 GACTGTAGACCGAACACTGTTC 58.693 50.000 11.37 11.37 0.00 3.18
2411 2780 2.691526 ACTGTAGACCGAACACTGTTCA 59.308 45.455 19.61 0.00 0.00 3.18
2412 2781 3.050619 CTGTAGACCGAACACTGTTCAC 58.949 50.000 19.61 11.20 0.00 3.18
2413 2782 2.049228 GTAGACCGAACACTGTTCACG 58.951 52.381 19.61 12.02 0.00 4.35
2414 2783 0.874607 AGACCGAACACTGTTCACGC 60.875 55.000 19.61 9.03 0.00 5.34
2415 2784 1.149361 GACCGAACACTGTTCACGCA 61.149 55.000 19.61 0.00 0.00 5.24
2416 2785 1.151777 ACCGAACACTGTTCACGCAG 61.152 55.000 19.61 5.08 41.92 5.18
2417 2786 0.874175 CCGAACACTGTTCACGCAGA 60.874 55.000 19.61 0.00 39.62 4.26
2418 2787 1.139989 CGAACACTGTTCACGCAGAT 58.860 50.000 19.61 0.00 39.62 2.90
2419 2788 1.125021 CGAACACTGTTCACGCAGATC 59.875 52.381 19.61 0.00 39.62 2.75
2420 2789 2.408050 GAACACTGTTCACGCAGATCT 58.592 47.619 15.77 0.00 39.62 2.75
2421 2790 1.788258 ACACTGTTCACGCAGATCTG 58.212 50.000 18.84 18.84 39.62 2.90
2422 2791 1.341209 ACACTGTTCACGCAGATCTGA 59.659 47.619 27.04 2.20 39.62 3.27
2423 2792 1.723542 CACTGTTCACGCAGATCTGAC 59.276 52.381 27.04 14.95 39.62 3.51
2424 2793 1.337260 ACTGTTCACGCAGATCTGACC 60.337 52.381 27.04 8.57 39.62 4.02
2425 2794 0.388520 TGTTCACGCAGATCTGACCG 60.389 55.000 27.04 21.77 0.00 4.79
2426 2795 0.388649 GTTCACGCAGATCTGACCGT 60.389 55.000 27.04 22.41 31.33 4.83
2427 2796 0.317160 TTCACGCAGATCTGACCGTT 59.683 50.000 27.04 8.98 29.34 4.44
2428 2797 0.388520 TCACGCAGATCTGACCGTTG 60.389 55.000 27.04 18.48 29.34 4.10
2429 2798 0.388520 CACGCAGATCTGACCGTTGA 60.389 55.000 27.04 0.00 29.34 3.18
2430 2799 0.532573 ACGCAGATCTGACCGTTGAT 59.467 50.000 27.04 2.60 0.00 2.57
2431 2800 1.066858 ACGCAGATCTGACCGTTGATT 60.067 47.619 27.04 2.24 0.00 2.57
2432 2801 1.590238 CGCAGATCTGACCGTTGATTC 59.410 52.381 27.04 3.34 0.00 2.52
2433 2802 2.736719 CGCAGATCTGACCGTTGATTCT 60.737 50.000 27.04 0.00 0.00 2.40
2434 2803 2.606725 GCAGATCTGACCGTTGATTCTG 59.393 50.000 27.04 0.00 0.00 3.02
2435 2804 3.193263 CAGATCTGACCGTTGATTCTGG 58.807 50.000 18.34 0.00 0.00 3.86
2436 2805 1.936547 GATCTGACCGTTGATTCTGGC 59.063 52.381 0.00 0.00 0.00 4.85
2437 2806 0.976641 TCTGACCGTTGATTCTGGCT 59.023 50.000 0.00 0.00 0.00 4.75
2438 2807 1.066858 TCTGACCGTTGATTCTGGCTC 60.067 52.381 0.00 0.00 0.00 4.70
2439 2808 0.389817 TGACCGTTGATTCTGGCTCG 60.390 55.000 0.00 0.00 0.00 5.03
2440 2809 1.079127 ACCGTTGATTCTGGCTCGG 60.079 57.895 0.00 0.00 42.94 4.63
2441 2810 1.218047 CCGTTGATTCTGGCTCGGA 59.782 57.895 0.00 0.00 40.29 4.55
2442 2811 0.179073 CCGTTGATTCTGGCTCGGAT 60.179 55.000 0.00 0.00 40.29 4.18
2443 2812 0.933097 CGTTGATTCTGGCTCGGATG 59.067 55.000 0.00 0.00 0.00 3.51
2444 2813 1.303309 GTTGATTCTGGCTCGGATGG 58.697 55.000 0.00 0.00 0.00 3.51
2445 2814 0.911769 TTGATTCTGGCTCGGATGGT 59.088 50.000 0.00 0.00 0.00 3.55
2446 2815 0.178767 TGATTCTGGCTCGGATGGTG 59.821 55.000 0.00 0.00 0.00 4.17
2447 2816 0.179000 GATTCTGGCTCGGATGGTGT 59.821 55.000 0.00 0.00 0.00 4.16
2448 2817 0.107508 ATTCTGGCTCGGATGGTGTG 60.108 55.000 0.00 0.00 0.00 3.82
2449 2818 2.124983 CTGGCTCGGATGGTGTGG 60.125 66.667 0.00 0.00 0.00 4.17
2450 2819 2.606213 TGGCTCGGATGGTGTGGA 60.606 61.111 0.00 0.00 0.00 4.02
2451 2820 2.187946 GGCTCGGATGGTGTGGAG 59.812 66.667 0.00 0.00 0.00 3.86
2452 2821 2.359169 GGCTCGGATGGTGTGGAGA 61.359 63.158 0.00 0.00 0.00 3.71
2453 2822 1.142748 GCTCGGATGGTGTGGAGAG 59.857 63.158 0.00 0.00 0.00 3.20
2454 2823 1.323271 GCTCGGATGGTGTGGAGAGA 61.323 60.000 0.00 0.00 0.00 3.10
2455 2824 0.743688 CTCGGATGGTGTGGAGAGAG 59.256 60.000 0.00 0.00 0.00 3.20
2456 2825 0.684479 TCGGATGGTGTGGAGAGAGG 60.684 60.000 0.00 0.00 0.00 3.69
2457 2826 1.680522 CGGATGGTGTGGAGAGAGGG 61.681 65.000 0.00 0.00 0.00 4.30
2458 2827 1.341156 GGATGGTGTGGAGAGAGGGG 61.341 65.000 0.00 0.00 0.00 4.79
2459 2828 1.977293 GATGGTGTGGAGAGAGGGGC 61.977 65.000 0.00 0.00 0.00 5.80
2460 2829 3.403558 GGTGTGGAGAGAGGGGCC 61.404 72.222 0.00 0.00 0.00 5.80
2461 2830 2.607750 GTGTGGAGAGAGGGGCCA 60.608 66.667 4.39 0.00 0.00 5.36
2462 2831 2.284921 TGTGGAGAGAGGGGCCAG 60.285 66.667 4.39 0.00 31.18 4.85
2463 2832 2.284995 GTGGAGAGAGGGGCCAGT 60.285 66.667 4.39 0.00 31.18 4.00
2464 2833 2.039624 TGGAGAGAGGGGCCAGTC 59.960 66.667 4.39 0.49 0.00 3.51
2465 2834 2.039624 GGAGAGAGGGGCCAGTCA 59.960 66.667 4.39 0.00 0.00 3.41
2466 2835 2.363172 GGAGAGAGGGGCCAGTCAC 61.363 68.421 4.39 0.00 0.00 3.67
2467 2836 2.284995 AGAGAGGGGCCAGTCACC 60.285 66.667 4.39 0.00 0.00 4.02
2468 2837 3.775654 GAGAGGGGCCAGTCACCG 61.776 72.222 4.39 0.00 0.00 4.94
2469 2838 4.640690 AGAGGGGCCAGTCACCGT 62.641 66.667 4.39 0.00 0.00 4.83
2470 2839 2.682494 GAGGGGCCAGTCACCGTA 60.682 66.667 4.39 0.00 0.00 4.02
2471 2840 3.001406 AGGGGCCAGTCACCGTAC 61.001 66.667 4.39 0.00 0.00 3.67
2472 2841 3.001406 GGGGCCAGTCACCGTACT 61.001 66.667 4.39 0.00 0.00 2.73
2473 2842 2.264794 GGGCCAGTCACCGTACTG 59.735 66.667 4.39 0.00 45.33 2.74
2474 2843 2.580601 GGGCCAGTCACCGTACTGT 61.581 63.158 4.39 0.00 44.45 3.55
2475 2844 1.370064 GGCCAGTCACCGTACTGTT 59.630 57.895 0.00 0.00 44.45 3.16
2476 2845 0.669625 GGCCAGTCACCGTACTGTTC 60.670 60.000 0.00 1.85 44.45 3.18
2477 2846 1.007336 GCCAGTCACCGTACTGTTCG 61.007 60.000 0.00 0.00 44.45 3.95
2478 2847 0.313043 CCAGTCACCGTACTGTTCGT 59.687 55.000 6.10 0.00 44.45 3.85
2479 2848 1.665161 CCAGTCACCGTACTGTTCGTC 60.665 57.143 6.10 0.00 44.45 4.20
2480 2849 0.236711 AGTCACCGTACTGTTCGTCG 59.763 55.000 6.10 0.00 0.00 5.12
2481 2850 0.235665 GTCACCGTACTGTTCGTCGA 59.764 55.000 6.10 0.00 0.00 4.20
2482 2851 0.514255 TCACCGTACTGTTCGTCGAG 59.486 55.000 6.10 0.00 0.00 4.04
2483 2852 1.063951 CACCGTACTGTTCGTCGAGC 61.064 60.000 1.65 1.65 0.00 5.03
2484 2853 1.208358 CCGTACTGTTCGTCGAGCA 59.792 57.895 11.45 11.45 0.00 4.26
2485 2854 0.386352 CCGTACTGTTCGTCGAGCAA 60.386 55.000 12.97 0.00 0.00 3.91
2486 2855 0.975544 CGTACTGTTCGTCGAGCAAG 59.024 55.000 12.97 9.46 0.00 4.01
2487 2856 1.337821 GTACTGTTCGTCGAGCAAGG 58.662 55.000 12.97 5.15 0.00 3.61
2488 2857 0.388134 TACTGTTCGTCGAGCAAGGC 60.388 55.000 12.97 0.00 0.00 4.35
2489 2858 1.664649 CTGTTCGTCGAGCAAGGCA 60.665 57.895 12.97 0.00 0.00 4.75
2490 2859 1.891060 CTGTTCGTCGAGCAAGGCAC 61.891 60.000 12.97 0.00 0.00 5.01
2492 2861 1.664649 TTCGTCGAGCAAGGCACTG 60.665 57.895 0.00 0.00 40.86 3.66
2493 2862 3.114616 CGTCGAGCAAGGCACTGG 61.115 66.667 0.00 0.00 40.86 4.00
2494 2863 2.343758 GTCGAGCAAGGCACTGGA 59.656 61.111 0.00 0.00 40.86 3.86
2495 2864 1.078848 GTCGAGCAAGGCACTGGAT 60.079 57.895 0.00 0.00 40.86 3.41
2496 2865 1.086634 GTCGAGCAAGGCACTGGATC 61.087 60.000 0.00 0.00 42.27 3.36
2497 2866 1.220206 CGAGCAAGGCACTGGATCT 59.780 57.895 0.00 0.00 43.79 2.75
2498 2867 0.809241 CGAGCAAGGCACTGGATCTC 60.809 60.000 0.00 0.00 43.79 2.75
2499 2868 0.251354 GAGCAAGGCACTGGATCTCA 59.749 55.000 0.00 0.00 42.45 3.27
2500 2869 0.917533 AGCAAGGCACTGGATCTCAT 59.082 50.000 0.00 0.00 40.86 2.90
2501 2870 1.284198 AGCAAGGCACTGGATCTCATT 59.716 47.619 0.00 0.00 40.86 2.57
2502 2871 1.674962 GCAAGGCACTGGATCTCATTC 59.325 52.381 0.00 0.00 40.86 2.67
2503 2872 2.295885 CAAGGCACTGGATCTCATTCC 58.704 52.381 0.00 0.00 40.86 3.01
2504 2873 1.588239 AGGCACTGGATCTCATTCCA 58.412 50.000 0.00 0.00 43.56 3.53
2505 2874 2.133520 AGGCACTGGATCTCATTCCAT 58.866 47.619 0.00 0.00 44.66 3.41
2506 2875 3.321039 AGGCACTGGATCTCATTCCATA 58.679 45.455 0.00 0.00 44.66 2.74
2507 2876 3.915073 AGGCACTGGATCTCATTCCATAT 59.085 43.478 0.00 0.00 44.66 1.78
2508 2877 5.096521 AGGCACTGGATCTCATTCCATATA 58.903 41.667 0.00 0.00 44.66 0.86
2532 3102 3.785859 GGCAGCCTCATCACGGGA 61.786 66.667 3.29 0.00 0.00 5.14
2533 3103 2.268920 GCAGCCTCATCACGGGAA 59.731 61.111 0.00 0.00 0.00 3.97
2561 3162 4.694987 ACCCCGCCCAAACCCATG 62.695 66.667 0.00 0.00 0.00 3.66
2573 3174 3.250521 CCAAACCCATGTGCAATGTTTTC 59.749 43.478 0.00 0.00 0.00 2.29
2579 3180 4.451774 CCCATGTGCAATGTTTTCGAAAAT 59.548 37.500 24.93 8.69 0.00 1.82
2603 3204 6.059484 TGTCCCTCTATTTCTTTGAAAACGT 58.941 36.000 0.00 0.00 0.00 3.99
2607 3208 5.390567 CCTCTATTTCTTTGAAAACGTCCCG 60.391 44.000 0.00 0.00 0.00 5.14
2622 3223 2.819595 CCGACGCCATCACCCTTG 60.820 66.667 0.00 0.00 0.00 3.61
2634 3235 2.832838 TCACCCTTGGAGCATCTCTAA 58.167 47.619 0.00 0.00 33.73 2.10
2658 3273 1.226184 CGACCCGCAAAATAACCGC 60.226 57.895 0.00 0.00 0.00 5.68
2659 3274 1.138036 GACCCGCAAAATAACCGCC 59.862 57.895 0.00 0.00 0.00 6.13
2666 3281 2.521996 GCAAAATAACCGCCCGTTTAG 58.478 47.619 0.00 0.00 35.79 1.85
2677 3292 1.673009 CCGTTTAGGCTTTCGGGCA 60.673 57.895 14.00 0.00 43.56 5.36
2678 3293 1.238625 CCGTTTAGGCTTTCGGGCAA 61.239 55.000 14.00 0.00 43.56 4.52
2702 3317 2.664402 AAGTGGCCTGATCAAACACT 57.336 45.000 16.52 16.52 43.61 3.55
2703 3318 1.901591 AGTGGCCTGATCAAACACTG 58.098 50.000 19.75 0.00 40.56 3.66
2704 3319 1.143684 AGTGGCCTGATCAAACACTGT 59.856 47.619 19.75 3.90 40.56 3.55
2708 3323 1.195448 GCCTGATCAAACACTGTGTCG 59.805 52.381 14.68 8.82 0.00 4.35
2714 3329 1.885850 AAACACTGTGTCGACCCGC 60.886 57.895 14.68 4.00 0.00 6.13
2741 3356 2.645192 AAAAAGGATTGCGGGGCGG 61.645 57.895 0.00 0.00 0.00 6.13
2752 3367 2.683572 GGGGCGGGGCAAATCTTT 60.684 61.111 0.00 0.00 0.00 2.52
2794 3409 4.791069 GTGGGAGGCCGACCCCTA 62.791 72.222 29.31 15.19 46.21 3.53
2807 3433 0.105453 ACCCCTATCGGCTGTGAGAT 60.105 55.000 0.00 0.00 0.00 2.75
2812 3438 2.158900 CCTATCGGCTGTGAGATTTGGT 60.159 50.000 0.00 0.00 0.00 3.67
2813 3439 1.742761 ATCGGCTGTGAGATTTGGTG 58.257 50.000 0.00 0.00 0.00 4.17
2829 3455 1.683441 GTGGGAGGGACATTTCCGT 59.317 57.895 0.00 0.00 43.94 4.69
2833 3459 1.079405 GAGGGACATTTCCGTGCGA 60.079 57.895 0.00 0.00 43.94 5.10
2834 3460 0.462047 GAGGGACATTTCCGTGCGAT 60.462 55.000 0.00 0.00 43.94 4.58
2878 3504 2.359975 GCCAACAACCTCCCTCCG 60.360 66.667 0.00 0.00 0.00 4.63
2935 3561 0.259647 CCATGGAAGCCTCCCAATCA 59.740 55.000 5.56 0.00 41.64 2.57
2938 3564 0.181114 TGGAAGCCTCCCAATCATCG 59.819 55.000 0.00 0.00 41.64 3.84
2951 3577 1.604147 ATCATCGCCTGTCACCGTGA 61.604 55.000 0.00 0.00 0.00 4.35
2953 3579 0.948623 CATCGCCTGTCACCGTGAAA 60.949 55.000 1.88 0.00 0.00 2.69
2955 3581 1.594293 CGCCTGTCACCGTGAAAGT 60.594 57.895 16.13 0.00 29.59 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.077184 CCGAGCTGTAACGGGCCA 62.077 66.667 4.39 0.00 44.59 5.36
35 36 3.368116 GCTCGCCTAATTATCATACCGGT 60.368 47.826 13.98 13.98 0.00 5.28
493 514 4.792513 AGCATCCATCCATCTTCTTTCT 57.207 40.909 0.00 0.00 0.00 2.52
718 739 1.031235 TGTCCATTGTTGCCACAGTG 58.969 50.000 6.46 6.46 39.73 3.66
719 740 1.682854 CTTGTCCATTGTTGCCACAGT 59.317 47.619 0.00 0.00 33.22 3.55
720 741 1.000060 CCTTGTCCATTGTTGCCACAG 60.000 52.381 0.00 0.00 33.22 3.66
935 965 2.811317 CAGCGAGACGTCAAGGCC 60.811 66.667 19.50 0.00 0.00 5.19
1341 1582 3.668447 TGACTGAACCTCTTTGATGCTC 58.332 45.455 0.00 0.00 0.00 4.26
2138 2477 0.237498 GCTCGTTTTTGCTACGGCTT 59.763 50.000 0.00 0.00 39.38 4.35
2335 2704 3.182263 CCTTCCCCCACACACCCA 61.182 66.667 0.00 0.00 0.00 4.51
2338 2707 2.034221 GAGCCTTCCCCCACACAC 59.966 66.667 0.00 0.00 0.00 3.82
2339 2708 3.256960 GGAGCCTTCCCCCACACA 61.257 66.667 0.00 0.00 37.53 3.72
2340 2709 2.155197 ATTGGAGCCTTCCCCCACAC 62.155 60.000 0.00 0.00 43.33 3.82
2341 2710 1.856873 ATTGGAGCCTTCCCCCACA 60.857 57.895 0.00 0.00 43.33 4.17
2342 2711 1.076705 GATTGGAGCCTTCCCCCAC 60.077 63.158 0.00 0.00 43.33 4.61
2343 2712 2.679342 CGATTGGAGCCTTCCCCCA 61.679 63.158 0.00 0.00 43.33 4.96
2344 2713 1.921869 TTCGATTGGAGCCTTCCCCC 61.922 60.000 0.00 0.00 43.33 5.40
2345 2714 0.183731 ATTCGATTGGAGCCTTCCCC 59.816 55.000 0.00 0.00 43.33 4.81
2347 2716 3.134458 CAGTATTCGATTGGAGCCTTCC 58.866 50.000 0.00 0.00 44.31 3.46
2350 2719 3.243907 GCTACAGTATTCGATTGGAGCCT 60.244 47.826 10.99 0.00 44.25 4.58
2351 2720 3.060602 GCTACAGTATTCGATTGGAGCC 58.939 50.000 10.99 0.00 44.25 4.70
2352 2721 2.726760 CGCTACAGTATTCGATTGGAGC 59.273 50.000 11.72 11.72 46.05 4.70
2353 2722 2.726760 GCGCTACAGTATTCGATTGGAG 59.273 50.000 0.00 0.00 0.00 3.86
2355 2724 2.218759 GTGCGCTACAGTATTCGATTGG 59.781 50.000 9.73 0.00 0.00 3.16
2356 2725 2.857748 TGTGCGCTACAGTATTCGATTG 59.142 45.455 9.73 0.00 33.42 2.67
2357 2726 3.159353 TGTGCGCTACAGTATTCGATT 57.841 42.857 9.73 0.00 33.42 3.34
2358 2727 2.858344 GTTGTGCGCTACAGTATTCGAT 59.142 45.455 9.73 0.00 41.10 3.59
2360 2729 1.989864 TGTTGTGCGCTACAGTATTCG 59.010 47.619 9.73 0.00 41.10 3.34
2361 2730 2.993899 AGTGTTGTGCGCTACAGTATTC 59.006 45.455 18.56 5.95 41.10 1.75
2362 2731 2.736721 CAGTGTTGTGCGCTACAGTATT 59.263 45.455 19.36 2.83 41.10 1.89
2363 2732 2.288825 ACAGTGTTGTGCGCTACAGTAT 60.289 45.455 19.36 8.13 41.10 2.12
2365 2734 0.179084 ACAGTGTTGTGCGCTACAGT 60.179 50.000 14.81 14.97 41.10 3.55
2366 2735 1.455786 GTACAGTGTTGTGCGCTACAG 59.544 52.381 14.81 7.11 41.10 2.74
2374 2743 1.202486 ACAGTCCCGTACAGTGTTGTG 60.202 52.381 0.00 0.00 38.23 3.33
2375 2744 1.117150 ACAGTCCCGTACAGTGTTGT 58.883 50.000 0.00 0.00 41.39 3.32
2376 2745 2.555325 TCTACAGTCCCGTACAGTGTTG 59.445 50.000 0.00 0.00 0.00 3.33
2377 2746 2.555757 GTCTACAGTCCCGTACAGTGTT 59.444 50.000 0.00 0.00 0.00 3.32
2378 2747 2.157738 GTCTACAGTCCCGTACAGTGT 58.842 52.381 0.00 0.00 0.00 3.55
2379 2748 1.471684 GGTCTACAGTCCCGTACAGTG 59.528 57.143 0.00 0.00 0.00 3.66
2381 2750 0.731417 CGGTCTACAGTCCCGTACAG 59.269 60.000 0.00 0.00 37.00 2.74
2382 2751 0.324614 TCGGTCTACAGTCCCGTACA 59.675 55.000 6.23 0.00 42.30 2.90
2384 2753 1.271325 TGTTCGGTCTACAGTCCCGTA 60.271 52.381 6.23 0.00 42.30 4.02
2386 2755 0.109412 GTGTTCGGTCTACAGTCCCG 60.109 60.000 0.00 0.00 43.03 5.14
2387 2756 1.067776 CAGTGTTCGGTCTACAGTCCC 60.068 57.143 0.00 0.00 0.00 4.46
2388 2757 1.612463 ACAGTGTTCGGTCTACAGTCC 59.388 52.381 0.00 0.00 0.00 3.85
2390 2759 2.691526 TGAACAGTGTTCGGTCTACAGT 59.308 45.455 26.59 0.00 0.00 3.55
2391 2760 3.050619 GTGAACAGTGTTCGGTCTACAG 58.949 50.000 26.59 0.00 0.00 2.74
2392 2761 2.542205 CGTGAACAGTGTTCGGTCTACA 60.542 50.000 26.59 9.02 0.00 2.74
2393 2762 2.049228 CGTGAACAGTGTTCGGTCTAC 58.951 52.381 26.59 18.68 0.00 2.59
2394 2763 1.601162 GCGTGAACAGTGTTCGGTCTA 60.601 52.381 26.59 9.78 0.00 2.59
2395 2764 0.874607 GCGTGAACAGTGTTCGGTCT 60.875 55.000 26.59 0.00 0.00 3.85
2396 2765 1.149361 TGCGTGAACAGTGTTCGGTC 61.149 55.000 26.59 18.86 0.00 4.79
2397 2766 1.151777 CTGCGTGAACAGTGTTCGGT 61.152 55.000 26.59 0.00 32.78 4.69
2398 2767 0.874175 TCTGCGTGAACAGTGTTCGG 60.874 55.000 26.59 21.93 38.84 4.30
2399 2768 1.125021 GATCTGCGTGAACAGTGTTCG 59.875 52.381 26.59 19.15 38.84 3.95
2400 2769 2.156504 CAGATCTGCGTGAACAGTGTTC 59.843 50.000 25.99 25.99 38.84 3.18
2401 2770 2.138320 CAGATCTGCGTGAACAGTGTT 58.862 47.619 10.38 8.61 38.84 3.32
2402 2771 1.341209 TCAGATCTGCGTGAACAGTGT 59.659 47.619 18.36 0.00 38.84 3.55
2403 2772 1.723542 GTCAGATCTGCGTGAACAGTG 59.276 52.381 18.36 0.00 38.84 3.66
2404 2773 1.337260 GGTCAGATCTGCGTGAACAGT 60.337 52.381 18.36 0.00 38.84 3.55
2405 2774 1.354040 GGTCAGATCTGCGTGAACAG 58.646 55.000 18.36 0.00 39.12 3.16
2406 2775 0.388520 CGGTCAGATCTGCGTGAACA 60.389 55.000 18.36 0.00 30.20 3.18
2407 2776 0.388649 ACGGTCAGATCTGCGTGAAC 60.389 55.000 22.38 13.54 30.38 3.18
2408 2777 0.317160 AACGGTCAGATCTGCGTGAA 59.683 50.000 23.32 3.33 31.57 3.18
2409 2778 0.388520 CAACGGTCAGATCTGCGTGA 60.389 55.000 23.32 3.95 31.57 4.35
2410 2779 0.388520 TCAACGGTCAGATCTGCGTG 60.389 55.000 23.32 17.85 31.57 5.34
2411 2780 0.532573 ATCAACGGTCAGATCTGCGT 59.467 50.000 18.36 18.66 32.27 5.24
2412 2781 1.590238 GAATCAACGGTCAGATCTGCG 59.410 52.381 18.36 18.01 0.00 5.18
2413 2782 2.606725 CAGAATCAACGGTCAGATCTGC 59.393 50.000 18.36 12.59 0.00 4.26
2414 2783 3.193263 CCAGAATCAACGGTCAGATCTG 58.807 50.000 17.07 17.07 0.00 2.90
2415 2784 2.419297 GCCAGAATCAACGGTCAGATCT 60.419 50.000 0.00 0.00 0.00 2.75
2416 2785 1.936547 GCCAGAATCAACGGTCAGATC 59.063 52.381 0.00 0.00 0.00 2.75
2417 2786 1.556911 AGCCAGAATCAACGGTCAGAT 59.443 47.619 0.00 0.00 0.00 2.90
2418 2787 0.976641 AGCCAGAATCAACGGTCAGA 59.023 50.000 0.00 0.00 0.00 3.27
2419 2788 1.363744 GAGCCAGAATCAACGGTCAG 58.636 55.000 0.00 0.00 0.00 3.51
2420 2789 0.389817 CGAGCCAGAATCAACGGTCA 60.390 55.000 0.00 0.00 0.00 4.02
2421 2790 1.084370 CCGAGCCAGAATCAACGGTC 61.084 60.000 0.00 0.00 36.38 4.79
2422 2791 1.079127 CCGAGCCAGAATCAACGGT 60.079 57.895 0.00 0.00 36.38 4.83
2423 2792 0.179073 ATCCGAGCCAGAATCAACGG 60.179 55.000 0.00 0.00 41.39 4.44
2424 2793 0.933097 CATCCGAGCCAGAATCAACG 59.067 55.000 0.00 0.00 0.00 4.10
2425 2794 1.303309 CCATCCGAGCCAGAATCAAC 58.697 55.000 0.00 0.00 0.00 3.18
2426 2795 0.911769 ACCATCCGAGCCAGAATCAA 59.088 50.000 0.00 0.00 0.00 2.57
2427 2796 0.178767 CACCATCCGAGCCAGAATCA 59.821 55.000 0.00 0.00 0.00 2.57
2428 2797 0.179000 ACACCATCCGAGCCAGAATC 59.821 55.000 0.00 0.00 0.00 2.52
2429 2798 0.107508 CACACCATCCGAGCCAGAAT 60.108 55.000 0.00 0.00 0.00 2.40
2430 2799 1.296392 CACACCATCCGAGCCAGAA 59.704 57.895 0.00 0.00 0.00 3.02
2431 2800 2.659063 CCACACCATCCGAGCCAGA 61.659 63.158 0.00 0.00 0.00 3.86
2432 2801 2.124983 CCACACCATCCGAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
2433 2802 2.606213 TCCACACCATCCGAGCCA 60.606 61.111 0.00 0.00 0.00 4.75
2434 2803 2.187946 CTCCACACCATCCGAGCC 59.812 66.667 0.00 0.00 0.00 4.70
2435 2804 1.142748 CTCTCCACACCATCCGAGC 59.857 63.158 0.00 0.00 0.00 5.03
2436 2805 0.743688 CTCTCTCCACACCATCCGAG 59.256 60.000 0.00 0.00 0.00 4.63
2437 2806 0.684479 CCTCTCTCCACACCATCCGA 60.684 60.000 0.00 0.00 0.00 4.55
2438 2807 1.680522 CCCTCTCTCCACACCATCCG 61.681 65.000 0.00 0.00 0.00 4.18
2439 2808 1.341156 CCCCTCTCTCCACACCATCC 61.341 65.000 0.00 0.00 0.00 3.51
2440 2809 1.977293 GCCCCTCTCTCCACACCATC 61.977 65.000 0.00 0.00 0.00 3.51
2441 2810 1.997874 GCCCCTCTCTCCACACCAT 60.998 63.158 0.00 0.00 0.00 3.55
2442 2811 2.607750 GCCCCTCTCTCCACACCA 60.608 66.667 0.00 0.00 0.00 4.17
2443 2812 3.403558 GGCCCCTCTCTCCACACC 61.404 72.222 0.00 0.00 0.00 4.16
2444 2813 2.607750 TGGCCCCTCTCTCCACAC 60.608 66.667 0.00 0.00 0.00 3.82
2445 2814 2.284921 CTGGCCCCTCTCTCCACA 60.285 66.667 0.00 0.00 0.00 4.17
2446 2815 2.284995 ACTGGCCCCTCTCTCCAC 60.285 66.667 0.00 0.00 0.00 4.02
2447 2816 2.039624 GACTGGCCCCTCTCTCCA 59.960 66.667 0.00 0.00 0.00 3.86
2448 2817 2.039624 TGACTGGCCCCTCTCTCC 59.960 66.667 0.00 0.00 0.00 3.71
2449 2818 2.363172 GGTGACTGGCCCCTCTCTC 61.363 68.421 0.00 0.00 0.00 3.20
2450 2819 2.284995 GGTGACTGGCCCCTCTCT 60.285 66.667 0.00 0.00 0.00 3.10
2451 2820 3.775654 CGGTGACTGGCCCCTCTC 61.776 72.222 0.00 0.00 0.00 3.20
2452 2821 3.233919 TACGGTGACTGGCCCCTCT 62.234 63.158 0.00 0.00 0.00 3.69
2453 2822 2.682494 TACGGTGACTGGCCCCTC 60.682 66.667 0.00 0.00 0.00 4.30
2454 2823 3.001406 GTACGGTGACTGGCCCCT 61.001 66.667 0.00 0.00 0.00 4.79
2455 2824 3.001406 AGTACGGTGACTGGCCCC 61.001 66.667 0.00 0.00 0.00 5.80
2456 2825 2.264794 CAGTACGGTGACTGGCCC 59.735 66.667 0.00 0.00 42.68 5.80
2461 2830 0.236711 CGACGAACAGTACGGTGACT 59.763 55.000 0.00 0.00 34.93 3.41
2462 2831 0.235665 TCGACGAACAGTACGGTGAC 59.764 55.000 0.00 0.00 34.93 3.67
2463 2832 0.514255 CTCGACGAACAGTACGGTGA 59.486 55.000 0.00 0.00 34.93 4.02
2464 2833 1.063951 GCTCGACGAACAGTACGGTG 61.064 60.000 0.00 0.00 34.93 4.94
2465 2834 1.208614 GCTCGACGAACAGTACGGT 59.791 57.895 0.00 0.00 34.93 4.83
2466 2835 0.386352 TTGCTCGACGAACAGTACGG 60.386 55.000 0.00 0.00 34.93 4.02
2467 2836 0.975544 CTTGCTCGACGAACAGTACG 59.024 55.000 0.00 0.00 0.00 3.67
2468 2837 1.337821 CCTTGCTCGACGAACAGTAC 58.662 55.000 0.00 0.00 0.00 2.73
2469 2838 0.388134 GCCTTGCTCGACGAACAGTA 60.388 55.000 0.00 0.00 0.00 2.74
2470 2839 1.664965 GCCTTGCTCGACGAACAGT 60.665 57.895 0.00 0.00 0.00 3.55
2471 2840 1.664649 TGCCTTGCTCGACGAACAG 60.665 57.895 0.00 0.00 0.00 3.16
2472 2841 1.954146 GTGCCTTGCTCGACGAACA 60.954 57.895 0.00 0.00 0.00 3.18
2473 2842 1.664965 AGTGCCTTGCTCGACGAAC 60.665 57.895 0.00 0.00 0.00 3.95
2474 2843 1.664649 CAGTGCCTTGCTCGACGAA 60.665 57.895 0.00 0.00 0.00 3.85
2475 2844 2.049156 CAGTGCCTTGCTCGACGA 60.049 61.111 0.00 0.00 0.00 4.20
2476 2845 2.842394 ATCCAGTGCCTTGCTCGACG 62.842 60.000 0.00 0.00 0.00 5.12
2477 2846 1.078848 ATCCAGTGCCTTGCTCGAC 60.079 57.895 0.00 0.00 0.00 4.20
2478 2847 1.219124 GATCCAGTGCCTTGCTCGA 59.781 57.895 0.00 0.00 0.00 4.04
2479 2848 0.809241 GAGATCCAGTGCCTTGCTCG 60.809 60.000 0.00 0.00 0.00 5.03
2480 2849 0.251354 TGAGATCCAGTGCCTTGCTC 59.749 55.000 0.00 0.00 0.00 4.26
2481 2850 0.917533 ATGAGATCCAGTGCCTTGCT 59.082 50.000 0.00 0.00 0.00 3.91
2482 2851 1.674962 GAATGAGATCCAGTGCCTTGC 59.325 52.381 0.00 0.00 0.00 4.01
2483 2852 2.295885 GGAATGAGATCCAGTGCCTTG 58.704 52.381 0.00 0.00 39.42 3.61
2484 2853 1.918262 TGGAATGAGATCCAGTGCCTT 59.082 47.619 0.00 0.00 44.52 4.35
2485 2854 1.588239 TGGAATGAGATCCAGTGCCT 58.412 50.000 0.00 0.00 44.52 4.75
2492 2861 6.407979 GCCTCCTCTTATATGGAATGAGATCC 60.408 46.154 0.00 0.00 40.10 3.36
2493 2862 6.155910 TGCCTCCTCTTATATGGAATGAGATC 59.844 42.308 0.00 0.00 31.23 2.75
2494 2863 6.028131 TGCCTCCTCTTATATGGAATGAGAT 58.972 40.000 0.00 0.00 31.23 2.75
2495 2864 5.406163 TGCCTCCTCTTATATGGAATGAGA 58.594 41.667 0.00 0.00 31.23 3.27
2496 2865 5.732633 CTGCCTCCTCTTATATGGAATGAG 58.267 45.833 0.00 0.00 31.23 2.90
2497 2866 4.019860 GCTGCCTCCTCTTATATGGAATGA 60.020 45.833 0.00 0.00 31.23 2.57
2498 2867 4.260170 GCTGCCTCCTCTTATATGGAATG 58.740 47.826 0.00 0.00 31.23 2.67
2499 2868 3.265479 GGCTGCCTCCTCTTATATGGAAT 59.735 47.826 12.43 0.00 31.23 3.01
2500 2869 2.639839 GGCTGCCTCCTCTTATATGGAA 59.360 50.000 12.43 0.00 31.23 3.53
2501 2870 2.158097 AGGCTGCCTCCTCTTATATGGA 60.158 50.000 17.22 0.00 0.00 3.41
2502 2871 2.264455 AGGCTGCCTCCTCTTATATGG 58.736 52.381 17.22 0.00 0.00 2.74
2559 3160 5.177327 GGACATTTTCGAAAACATTGCACAT 59.823 36.000 24.68 3.70 0.00 3.21
2561 3162 4.084589 GGGACATTTTCGAAAACATTGCAC 60.085 41.667 24.68 15.48 0.00 4.57
2573 3174 7.377766 TCAAAGAAATAGAGGGACATTTTCG 57.622 36.000 0.00 0.00 32.84 3.46
2579 3180 6.059484 ACGTTTTCAAAGAAATAGAGGGACA 58.941 36.000 0.00 0.00 0.00 4.02
2607 3208 1.450312 CTCCAAGGGTGATGGCGTC 60.450 63.158 0.00 0.00 37.88 5.19
2611 3212 0.549950 AGATGCTCCAAGGGTGATGG 59.450 55.000 0.00 0.00 39.41 3.51
2614 3215 2.501723 GTTAGAGATGCTCCAAGGGTGA 59.498 50.000 0.00 0.00 0.00 4.02
2622 3223 0.872021 CGGCGTGTTAGAGATGCTCC 60.872 60.000 0.00 0.00 0.00 4.70
2659 3274 1.238625 TTGCCCGAAAGCCTAAACGG 61.239 55.000 0.00 0.00 44.16 4.44
2687 3302 1.537202 GACACAGTGTTTGATCAGGCC 59.463 52.381 7.86 0.00 0.00 5.19
2691 3306 2.479837 GGTCGACACAGTGTTTGATCA 58.520 47.619 18.91 0.00 0.00 2.92
2697 3312 2.279918 GCGGGTCGACACAGTGTT 60.280 61.111 19.62 0.00 0.00 3.32
2752 3367 2.093890 TGTATCTAAAGGTCGACGGCA 58.906 47.619 9.92 0.00 0.00 5.69
2754 3369 2.540361 CCGTGTATCTAAAGGTCGACGG 60.540 54.545 9.92 0.00 39.17 4.79
2756 3371 2.223665 CCCCGTGTATCTAAAGGTCGAC 60.224 54.545 7.13 7.13 0.00 4.20
2792 3407 2.868583 CACCAAATCTCACAGCCGATAG 59.131 50.000 0.00 0.00 0.00 2.08
2793 3408 2.419990 CCACCAAATCTCACAGCCGATA 60.420 50.000 0.00 0.00 0.00 2.92
2794 3409 1.679944 CCACCAAATCTCACAGCCGAT 60.680 52.381 0.00 0.00 0.00 4.18
2802 3428 0.991920 GTCCCTCCCACCAAATCTCA 59.008 55.000 0.00 0.00 0.00 3.27
2807 3433 1.203125 GGAAATGTCCCTCCCACCAAA 60.203 52.381 0.00 0.00 38.08 3.28
2812 3438 1.682849 CACGGAAATGTCCCTCCCA 59.317 57.895 0.00 0.00 41.44 4.37
2813 3439 1.749258 GCACGGAAATGTCCCTCCC 60.749 63.158 0.00 0.00 41.44 4.30
2833 3459 0.837940 GAAGGGGAAGCGGGAACTAT 59.162 55.000 0.00 0.00 0.00 2.12
2834 3460 1.269703 GGAAGGGGAAGCGGGAACTA 61.270 60.000 0.00 0.00 0.00 2.24
2885 3511 2.202932 CCGATGAAGGTGCTCCGG 60.203 66.667 0.00 0.00 39.05 5.14
2891 3517 0.462759 GAGGGAAGCCGATGAAGGTG 60.463 60.000 0.00 0.00 0.00 4.00
2897 3523 2.203126 GGCAGAGGGAAGCCGATG 60.203 66.667 0.00 0.00 41.70 3.84
2935 3561 0.670546 CTTTCACGGTGACAGGCGAT 60.671 55.000 10.97 0.00 0.00 4.58
2938 3564 0.531974 TGACTTTCACGGTGACAGGC 60.532 55.000 23.78 22.29 32.91 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.